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Enhancement-changed NCV threshold in low #110

Closed alieden closed 6 years ago

alieden commented 6 years ago

Oops, opened before I was finished with the title etc

alieden commented 6 years ago

In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21. These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow). It was just decided that these rules will be introduced in our LIMS starting on the 23rd of October. Given that, it would be great if you could make this change in the NIPT software at the same time or just prioritize this to be fixed asap after the 23rd. Sorry for the short heads up!

mayabrandi commented 6 years ago

No problem. Ill prioritise this and make sure its in place the 23/10.

/Maya

9 okt. 2018 kl. 17:24 skrev alieden notifications@github.com:

In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21. These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow). It was just decided that these rules will be introduced in our LIMS starting on the 23rd of October. Given that, it would be great if you could make this change in the NIPT software at the same time or just prioritize this to be fixed asap after the 23rd. Sorry for the short heads up!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-428236656, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3evPrvKetHWoX8Y_HX_sp7dxV0VDks5ujL_EgaJpZM4XTgfp.

alieden commented 6 years ago

Thanks!

Agne

10 okt. 2018 kl. 08:15 skrev mayabrandi notifications@github.com<mailto:notifications@github.com>:

No problem. Ill prioritise this and make sure its in place the 23/10.

/Maya

9 okt. 2018 kl. 17:24 skrev alieden notifications@github.com<mailto:notifications@github.com>:

In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21. These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow). It was just decided that these rules will be introduced in our LIMS starting on the 23rd of October. Given that, it would be great if you could make this change in the NIPT software at the same time or just prioritize this to be fixed asap after the 23rd. Sorry for the short heads up!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-428236656, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3evPrvKetHWoX8Y_HX_sp7dxV0VDks5ujL_EgaJpZM4XTgfp.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-428450812, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fBVVLOi5uF7R0KuXtp22_dvZDV1Xks5ujZCSgaJpZM4XTgfp.

mayabrandi commented 6 years ago

As always I need some clarification ;) Two question marks:

1) "In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21."

Do I understand you right if you want me lower the treshold to 2.5, for the samples that have a low fetal fraction only? In that case I wonder how you want that to be visualized. In eg a ncv_13 plot you want the yellow line to vary over the different samples?

2) "These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow)."

Samples are not automatically flagged yellow. They are set to yellow when you manually classify the sample as suspected.

alieden commented 6 years ago

  1. There would have to be another warning threshold line at 2,5 (i.e. three upper in total), if this looks ok? The same color as the one at 3,0 I think.

  2. Ok. Are you sure about this? But there is a flag in the warning column at least?

Thank you for looking at this with such short notice!

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 16 oktober 2018 12:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com Kopia: Agne Lieden Agne.Lieden@ki.se; Author author@noreply.github.com Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

As always I need some clarification ;) Two question marks:

  1. "In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21."

Do I understand you right if you want me lower the treshold to 2.5, for the samples that have a low fetal fraction only? In that case I wonder how you want that to be visualized. In eg a ncv_13 plot you want the yellow line to vary over the different samples?

  1. "These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow)."

Samples are not automatically flagged yellow. They are set to yellow when you manually classify the sample as suspected.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430190340, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fJ8cYk29ItIPM71VkGMLu4G0Guv0ks5ulbh2gaJpZM4XTgfp.

mayabrandi commented 6 years ago

Hi!

  1. There would have to be another warning threshold line at 2,5 (i.e. three upper in total), if this looks ok? The same color as the one at 3,0 I think.

Ok! Np.

  1. Ok. Are you sure about this? But there is a flag in the warning column at least?

Yes and yes there is a warning.

And to be super clear.. This is what you want:

If a sample has ff<5% then I warn for ncv13,ncv18,ncv21 > 2.5 If a sample has ff>5% then I warn for ncv13,ncv18,ncv21 > 3

Correct?

Thank you for looking at this with such short notice!

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 16 oktober 2018 12:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com Kopia: Agne Lieden Agne.Lieden@ki.se; Author author@noreply.github.com Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

As always I need some clarification ;) Two question marks:

  1. "In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21."

Do I understand you right if you want me lower the treshold to 2.5, for the samples that have a low fetal fraction only? In that case I wonder how you want that to be visualized. In eg a ncv_13 plot you want the yellow line to vary over the different samples?

  1. "These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow)."

Samples are not automatically flagged yellow. They are set to yellow when you manually classify the sample as suspected.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430190340, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fJ8cYk29ItIPM71VkGMLu4G0Guv0ks5ulbh2gaJpZM4XTgfp. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430527286, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3e5ig516xdi7yIdEsSjxgmtxBgxHks5uluHugaJpZM4XTgfp.

alieden commented 6 years ago

Yes but the rules should be

If a sample has ff ≤ 5%, then I warn for ncv21 ≥ 2.5

If a sample has ff >5%, then I warn for ncv21 ≥ 3.0

And then the same rules also applied for 13 and 18.

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 18 oktober 2018 13:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com Kopia: Agne Lieden Agne.Lieden@ki.se; Author author@noreply.github.com Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hi!

  1. There would have to be another warning threshold line at 2,5 (i.e. three upper in total), if this looks ok? The same color as the one at 3,0 I think.

Ok! Np.

  1. Ok. Are you sure about this? But there is a flag in the warning column at least?

Yes and yes there is a warning.

And to be super clear.. This is what you want:

If a sample has ff<5% then I warn for ncv13,ncv18,ncv21 > 2.5 If a sample has ff>5% then I warn for ncv13,ncv18,ncv21 > 3

Correct?

Thank you for looking at this with such short notice!

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 16 oktober 2018 12:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

As always I need some clarification ;) Two question marks:

  1. "In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21."

Do I understand you right if you want me lower the treshold to 2.5, for the samples that have a low fetal fraction only? In that case I wonder how you want that to be visualized. In eg a ncv_13 plot you want the yellow line to vary over the different samples?

  1. "These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow)."

Samples are not automatically flagged yellow. They are set to yellow when you manually classify the sample as suspected.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430190340, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fJ8cYk29ItIPM71VkGMLu4G0Guv0ks5ulbh2gaJpZM4XTgfp. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430527286, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3e5ig516xdi7yIdEsSjxgmtxBgxHks5uluHugaJpZM4XTgfp.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430977315, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fHa32sacKhvP7kCP9ZrW-EKpE02nks5umGmDgaJpZM4XTgfp.

mayabrandi commented 6 years ago

Hej. Måste bara kolla en grej till. Tröskeln för att varan för "low FF" är i nuläget 2%. Ska jag höja den till 5%?

19 okt. 2018 kl. 07:30 skrev alieden notifications@github.com:

Yes but the rules should be

If a sample has ff ≤ 5%, then I warn for ncv21 ≥ 2.5

If a sample has ff >5%, then I warn for ncv21 ≥ 3.0

And then the same rules also applied for 13 and 18.

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 18 oktober 2018 13:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com Kopia: Agne Lieden Agne.Lieden@ki.se; Author author@noreply.github.com Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hi!

  1. There would have to be another warning threshold line at 2,5 (i.e. three upper in total), if this looks ok? The same color as the one at 3,0 I think.

Ok! Np.

  1. Ok. Are you sure about this? But there is a flag in the warning column at least?

Yes and yes there is a warning.

And to be super clear.. This is what you want:

If a sample has ff<5% then I warn for ncv13,ncv18,ncv21 > 2.5 If a sample has ff>5% then I warn for ncv13,ncv18,ncv21 > 3

Correct?

Thank you for looking at this with such short notice!

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 16 oktober 2018 12:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

As always I need some clarification ;) Two question marks:

  1. "In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21."

Do I understand you right if you want me lower the treshold to 2.5, for the samples that have a low fetal fraction only? In that case I wonder how you want that to be visualized. In eg a ncv_13 plot you want the yellow line to vary over the different samples?

  1. "These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow)."

Samples are not automatically flagged yellow. They are set to yellow when you manually classify the sample as suspected.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430190340, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fJ8cYk29ItIPM71VkGMLu4G0Guv0ks5ulbh2gaJpZM4XTgfp. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430527286, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3e5ig516xdi7yIdEsSjxgmtxBgxHks5uluHugaJpZM4XTgfp.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430977315, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fHa32sacKhvP7kCP9ZrW-EKpE02nks5umGmDgaJpZM4XTgfp. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-431249340, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3W7CJ1ggOlwDyPMm-s4hH7SALau5ks5umWOAgaJpZM4XTgfp.

alieden commented 6 years ago

Nej, 2% är den minsta mängd som krävs för godkänd analys med normalfynd.

Jag tycker inte vi behöver flagga låg ff vid 5% (eller lägre) om det inte sammanfaller med ett NCV precis under 3 (som den nya regeln tar hand om).

Inser att det är lite rörigt, bra att du säger till om det inte verkar gå ihop. Vi kan ju faktiskt tänkt galet:)

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 19 oktober 2018 13:13 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com Kopia: Agne Lieden Agne.Lieden@ki.se; Author author@noreply.github.com Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hej. Måste bara kolla en grej till. Tröskeln för att varan för "low FF" är i nuläget 2%. Ska jag höja den till 5%?

19 okt. 2018 kl. 07:30 skrev alieden notifications@github.com:

Yes but the rules should be

If a sample has ff ≤ 5%, then I warn for ncv21 ≥ 2.5

If a sample has ff >5%, then I warn for ncv21 ≥ 3.0

And then the same rules also applied for 13 and 18.

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 18 oktober 2018 13:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com Kopia: Agne Lieden Agne.Lieden@ki.se; Author author@noreply.github.com Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hi!

  1. There would have to be another warning threshold line at 2,5 (i.e. three upper in total), if this looks ok? The same color as the one at 3,0 I think.

Ok! Np.

  1. Ok. Are you sure about this? But there is a flag in the warning column at least?

Yes and yes there is a warning.

And to be super clear.. This is what you want:

If a sample has ff<5% then I warn for ncv13,ncv18,ncv21 > 2.5 If a sample has ff>5% then I warn for ncv13,ncv18,ncv21 > 3

Correct?

Thank you for looking at this with such short notice!

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 16 oktober 2018 12:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

As always I need some clarification ;) Two question marks:

  1. "In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21."

Do I understand you right if you want me lower the treshold to 2.5, for the samples that have a low fetal fraction only? In that case I wonder how you want that to be visualized. In eg a ncv_13 plot you want the yellow line to vary over the different samples?

  1. "These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow)."

Samples are not automatically flagged yellow. They are set to yellow when you manually classify the sample as suspected.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430190340, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fJ8cYk29ItIPM71VkGMLu4G0Guv0ks5ulbh2gaJpZM4XTgfp. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430527286, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3e5ig516xdi7yIdEsSjxgmtxBgxHks5uluHugaJpZM4XTgfp.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430977315, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fHa32sacKhvP7kCP9ZrW-EKpE02nks5umGmDgaJpZM4XTgfp. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-431249340, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3W7CJ1ggOlwDyPMm-s4hH7SALau5ks5umWOAgaJpZM4XTgfp.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-431329130, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fJ968dbsh8us_OqGjaOBZ_7fk85Yks5umbO2gaJpZM4XTgfp.

mayabrandi commented 6 years ago

Okej.

I attach a screen shot where Ive manipulated the ncv18 data and ff data for four samples in our stage database. See if the warnings are as you expect.

19 okt. 2018 kl. 13:23 skrev alieden notifications@github.com:

Nej, 2% är den minsta mängd som krävs för godkänd analys med normalfynd.

Jag tycker inte vi behöver flagga låg ff vid 5% (eller lägre) om det inte sammanfaller med ett NCV precis under 3 (som den nya regeln tar hand om).

Inser att det är lite rörigt, bra att du säger till om det inte verkar gå ihop. Vi kan ju faktiskt tänkt galet:)

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 19 oktober 2018 13:13 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com Kopia: Agne Lieden Agne.Lieden@ki.se; Author author@noreply.github.com Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hej. Måste bara kolla en grej till. Tröskeln för att varan för "low FF" är i nuläget 2%. Ska jag höja den till 5%?

19 okt. 2018 kl. 07:30 skrev alieden notifications@github.com:

Yes but the rules should be

If a sample has ff ≤ 5%, then I warn for ncv21 ≥ 2.5

If a sample has ff >5%, then I warn for ncv21 ≥ 3.0

And then the same rules also applied for 13 and 18.

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 18 oktober 2018 13:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com Kopia: Agne Lieden Agne.Lieden@ki.se; Author author@noreply.github.com Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hi!

  1. There would have to be another warning threshold line at 2,5 (i.e. three upper in total), if this looks ok? The same color as the one at 3,0 I think.

Ok! Np.

  1. Ok. Are you sure about this? But there is a flag in the warning column at least?

Yes and yes there is a warning.

And to be super clear.. This is what you want:

If a sample has ff<5% then I warn for ncv13,ncv18,ncv21 > 2.5 If a sample has ff>5% then I warn for ncv13,ncv18,ncv21 > 3

Correct?

Thank you for looking at this with such short notice!

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 16 oktober 2018 12:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

As always I need some clarification ;) Two question marks:

  1. "In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21."

Do I understand you right if you want me lower the treshold to 2.5, for the samples that have a low fetal fraction only? In that case I wonder how you want that to be visualized. In eg a ncv_13 plot you want the yellow line to vary over the different samples?

  1. "These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow)."

Samples are not automatically flagged yellow. They are set to yellow when you manually classify the sample as suspected.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430190340, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fJ8cYk29ItIPM71VkGMLu4G0Guv0ks5ulbh2gaJpZM4XTgfp. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430527286, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3e5ig516xdi7yIdEsSjxgmtxBgxHks5uluHugaJpZM4XTgfp.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430977315, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fHa32sacKhvP7kCP9ZrW-EKpE02nks5umGmDgaJpZM4XTgfp. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-431249340, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3W7CJ1ggOlwDyPMm-s4hH7SALau5ks5umWOAgaJpZM4XTgfp.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-431329130, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fJ968dbsh8us_OqGjaOBZ_7fk85Yks5umbO2gaJpZM4XTgfp. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-431331559, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3VDrWYlKr7esjLnJbraDoc4gzZgyks5umbZKgaJpZM4XTgfp.

alieden commented 6 years ago

This looks correct.

However, I just realized that the best would be if the warning of low ff occurs at 3% or lower. This is becauses 4% is the lowest value allowed for a twin pregnancy i.e good if that is flagged since we only have manual checks for this.

Kr,

Agne

19 okt. 2018 kl. 14:40 skrev mayabrandi notifications@github.com<mailto:notifications@github.com>:

Okej.

I attach a screen shot where Ive manipulated the ncv18 data and ff data for four samples in our stage database. See if the warnings are as you expect.

19 okt. 2018 kl. 13:23 skrev alieden notifications@github.com<mailto:notifications@github.com>:

Nej, 2% är den minsta mängd som krävs för godkänd analys med normalfynd.

Jag tycker inte vi behöver flagga låg ff vid 5% (eller lägre) om det inte sammanfaller med ett NCV precis under 3 (som den nya regeln tar hand om).

Inser att det är lite rörigt, bra att du säger till om det inte verkar gå ihop. Vi kan ju faktiskt tänkt galet:)

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 19 oktober 2018 13:13 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hej. Måste bara kolla en grej till. Tröskeln för att varan för "low FF" är i nuläget 2%. Ska jag höja den till 5%?

19 okt. 2018 kl. 07:30 skrev alieden notifications@github.com<mailto:notifications@github.com>:

Yes but the rules should be

If a sample has ff ≤ 5%, then I warn for ncv21 ≥ 2.5

If a sample has ff >5%, then I warn for ncv21 ≥ 3.0

And then the same rules also applied for 13 and 18.

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 18 oktober 2018 13:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hi!

  1. There would have to be another warning threshold line at 2,5 (i.e. three upper in total), if this looks ok? The same color as the one at 3,0 I think.

Ok! Np.

  1. Ok. Are you sure about this? But there is a flag in the warning column at least?

Yes and yes there is a warning.

And to be super clear.. This is what you want:

If a sample has ff<5% then I warn for ncv13,ncv18,ncv21 > 2.5 If a sample has ff>5% then I warn for ncv13,ncv18,ncv21 > 3

Correct?

Thank you for looking at this with such short notice!

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 16 oktober 2018 12:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.commailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.semailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.commailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

As always I need some clarification ;) Two question marks:

  1. "In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21."

Do I understand you right if you want me lower the treshold to 2.5, for the samples that have a low fetal fraction only? In that case I wonder how you want that to be visualized. In eg a ncv_13 plot you want the yellow line to vary over the different samples?

  1. "These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow)."

Samples are not automatically flagged yellow. They are set to yellow when you manually classify the sample as suspected.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430190340, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fJ8cYk29ItIPM71VkGMLu4G0Guv0ks5ulbh2gaJpZM4XTgfp. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430527286, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3e5ig516xdi7yIdEsSjxgmtxBgxHks5uluHugaJpZM4XTgfp.

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mayabrandi commented 6 years ago

Hi!

Okej I changed the threshold for low ff from 2% to 3%.

The new updated version of the code is up and running on https://nipt-stage.scilifelab.se/NIPT/

Its running against our nipt-stage database so you can test things there without effecting production stuff.

Here https://nipt-stage.scilifelab.se/NIPT/batches/BH2375BCX2/ is the batch where I manipulated the data to visualise how the new thresholds work.

Please check that everything is as you wish now. Then Ill put this into production late this afternoon.

Okej?

Best,

Maya

19 okt. 2018 kl. 16:50 skrev alieden notifications@github.com:

This looks correct.

However, I just realized that the best would be if the warning of low ff occurs at 3% or lower. This is becauses 4% is the lowest value allowed for a twin pregnancy i.e good if that is flagged since we only have manual checks for this.

Kr,

Agne

19 okt. 2018 kl. 14:40 skrev mayabrandi notifications@github.com<mailto:notifications@github.com>:

Okej.

I attach a screen shot where Ive manipulated the ncv18 data and ff data for four samples in our stage database. See if the warnings are as you expect.

19 okt. 2018 kl. 13:23 skrev alieden notifications@github.com<mailto:notifications@github.com>:

Nej, 2% är den minsta mängd som krävs för godkänd analys med normalfynd.

Jag tycker inte vi behöver flagga låg ff vid 5% (eller lägre) om det inte sammanfaller med ett NCV precis under 3 (som den nya regeln tar hand om).

Inser att det är lite rörigt, bra att du säger till om det inte verkar gå ihop. Vi kan ju faktiskt tänkt galet:)

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 19 oktober 2018 13:13 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hej. Måste bara kolla en grej till. Tröskeln för att varan för "low FF" är i nuläget 2%. Ska jag höja den till 5%?

19 okt. 2018 kl. 07:30 skrev alieden notifications@github.com<mailto:notifications@github.com>:

Yes but the rules should be

If a sample has ff ≤ 5%, then I warn for ncv21 ≥ 2.5

If a sample has ff >5%, then I warn for ncv21 ≥ 3.0

And then the same rules also applied for 13 and 18.

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 18 oktober 2018 13:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hi!

  1. There would have to be another warning threshold line at 2,5 (i.e. three upper in total), if this looks ok? The same color as the one at 3,0 I think.

Ok! Np.

  1. Ok. Are you sure about this? But there is a flag in the warning column at least?

Yes and yes there is a warning.

And to be super clear.. This is what you want:

If a sample has ff<5% then I warn for ncv13,ncv18,ncv21 > 2.5 If a sample has ff>5% then I warn for ncv13,ncv18,ncv21 > 3

Correct?

Thank you for looking at this with such short notice!

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 16 oktober 2018 12:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.commailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.semailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.commailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

As always I need some clarification ;) Two question marks:

  1. "In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21."

Do I understand you right if you want me lower the treshold to 2.5, for the samples that have a low fetal fraction only? In that case I wonder how you want that to be visualized. In eg a ncv_13 plot you want the yellow line to vary over the different samples?

  1. "These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow)."

Samples are not automatically flagged yellow. They are set to yellow when you manually classify the sample as suspected.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430190340, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fJ8cYk29ItIPM71VkGMLu4G0Guv0ks5ulbh2gaJpZM4XTgfp. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430527286, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3e5ig516xdi7yIdEsSjxgmtxBgxHks5uluHugaJpZM4XTgfp.

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alieden commented 6 years ago

This looks correct.

However, perhaps the warning for low ff could be adjusted further as detailed below. This to clarify the warning in relation to the 2% threshold in singleton and 4% in twin pregnancies.

Below 2% = Low FF (all) 2% = Low FF (twin) 3% = Low FF (twin)

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 22 oktober 2018 18:43 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com Kopia: Agne Lieden Agne.Lieden@ki.se; Author author@noreply.github.com Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hi!

Okej I changed the threshold for low ff from 2% to 3%.

The new updated version of the code is up and running on https://nipt-stage.scilifelab.se/NIPT/

Its running against our nipt-stage database so you can test things there without effecting production stuff.

Here https://nipt-stage.scilifelab.se/NIPT/batches/BH2375BCX2/ is the batch where I manipulated the data to visualise how the new thresholds work.

Please check that everything is as you wish now. Then Ill put this into production late this afternoon.

Okej?

Best,

Maya

19 okt. 2018 kl. 16:50 skrev alieden notifications@github.com<mailto:notifications@github.com>:

This looks correct.

However, I just realized that the best would be if the warning of low ff occurs at 3% or lower. This is becauses 4% is the lowest value allowed for a twin pregnancy i.e good if that is flagged since we only have manual checks for this.

Kr,

Agne

19 okt. 2018 kl. 14:40 skrev mayabrandi notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>>:

Okej.

I attach a screen shot where Ive manipulated the ncv18 data and ff data for four samples in our stage database. See if the warnings are as you expect.

19 okt. 2018 kl. 13:23 skrev alieden notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>>:

Nej, 2% är den minsta mängd som krävs för godkänd analys med normalfynd.

Jag tycker inte vi behöver flagga låg ff vid 5% (eller lägre) om det inte sammanfaller med ett NCV precis under 3 (som den nya regeln tar hand om).

Inser att det är lite rörigt, bra att du säger till om det inte verkar gå ihop. Vi kan ju faktiskt tänkt galet:)

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 19 oktober 2018 13:13 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com<mailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com>> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se>>; Author author@noreply.github.com<mailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com>> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hej. Måste bara kolla en grej till. Tröskeln för att varan för "low FF" är i nuläget 2%. Ska jag höja den till 5%?

19 okt. 2018 kl. 07:30 skrev alieden notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>>:

Yes but the rules should be

If a sample has ff ≤ 5%, then I warn for ncv21 ≥ 2.5

If a sample has ff >5%, then I warn for ncv21 ≥ 3.0

And then the same rules also applied for 13 and 18.

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 18 oktober 2018 13:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com<mailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com>> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se>>; Author author@noreply.github.com<mailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com>> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hi!

  1. There would have to be another warning threshold line at 2,5 (i.e. three upper in total), if this looks ok? The same color as the one at 3,0 I think.

Ok! Np.

  1. Ok. Are you sure about this? But there is a flag in the warning column at least?

Yes and yes there is a warning.

And to be super clear.. This is what you want:

If a sample has ff<5% then I warn for ncv13,ncv18,ncv21 > 2.5 If a sample has ff>5% then I warn for ncv13,ncv18,ncv21 > 3

Correct?

Thank you for looking at this with such short notice!

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 16 oktober 2018 12:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com<mailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com>mailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se>mailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com>mailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

As always I need some clarification ;) Two question marks:

  1. "In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21."

Do I understand you right if you want me lower the treshold to 2.5, for the samples that have a low fetal fraction only? In that case I wonder how you want that to be visualized. In eg a ncv_13 plot you want the yellow line to vary over the different samples?

  1. "These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow)."

Samples are not automatically flagged yellow. They are set to yellow when you manually classify the sample as suspected.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430190340, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fJ8cYk29ItIPM71VkGMLu4G0Guv0ks5ulbh2gaJpZM4XTgfp. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430527286, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3e5ig516xdi7yIdEsSjxgmtxBgxHks5uluHugaJpZM4XTgfp.

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mayabrandi commented 6 years ago

Hi.

Ill push the new version into production and set the new suggestion as a separate issue. I don’t have time to work more on this today unfortunately.

Best,

Maya

23 okt. 2018 kl. 07:40 skrev alieden notifications@github.com:

This looks correct.

However, perhaps the warning for low ff could be adjusted further as detailed below. This to clarify the warning in relation to the 2% threshold in singleton and 4% in twin pregnancies.

Below 2% = Low FF (all) 2% = Low FF (twin) 3% = Low FF (twin)

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 22 oktober 2018 18:43 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com Kopia: Agne Lieden Agne.Lieden@ki.se; Author author@noreply.github.com Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hi!

Okej I changed the threshold for low ff from 2% to 3%.

The new updated version of the code is up and running on https://nipt-stage.scilifelab.se/NIPT/

Its running against our nipt-stage database so you can test things there without effecting production stuff.

Here https://nipt-stage.scilifelab.se/NIPT/batches/BH2375BCX2/ is the batch where I manipulated the data to visualise how the new thresholds work.

Please check that everything is as you wish now. Then Ill put this into production late this afternoon.

Okej?

Best,

Maya

19 okt. 2018 kl. 16:50 skrev alieden notifications@github.com<mailto:notifications@github.com>:

This looks correct.

However, I just realized that the best would be if the warning of low ff occurs at 3% or lower. This is becauses 4% is the lowest value allowed for a twin pregnancy i.e good if that is flagged since we only have manual checks for this.

Kr,

Agne

19 okt. 2018 kl. 14:40 skrev mayabrandi notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>>:

Okej.

I attach a screen shot where Ive manipulated the ncv18 data and ff data for four samples in our stage database. See if the warnings are as you expect.

19 okt. 2018 kl. 13:23 skrev alieden notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>>:

Nej, 2% är den minsta mängd som krävs för godkänd analys med normalfynd.

Jag tycker inte vi behöver flagga låg ff vid 5% (eller lägre) om det inte sammanfaller med ett NCV precis under 3 (som den nya regeln tar hand om).

Inser att det är lite rörigt, bra att du säger till om det inte verkar gå ihop. Vi kan ju faktiskt tänkt galet:)

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 19 oktober 2018 13:13 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com<mailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com>> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se>>; Author author@noreply.github.com<mailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com>> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hej. Måste bara kolla en grej till. Tröskeln för att varan för "low FF" är i nuläget 2%. Ska jag höja den till 5%?

19 okt. 2018 kl. 07:30 skrev alieden notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>>:

Yes but the rules should be

If a sample has ff ≤ 5%, then I warn for ncv21 ≥ 2.5

If a sample has ff >5%, then I warn for ncv21 ≥ 3.0

And then the same rules also applied for 13 and 18.

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 18 oktober 2018 13:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com<mailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com>> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se>>; Author author@noreply.github.com<mailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com>> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hi!

  1. There would have to be another warning threshold line at 2,5 (i.e. three upper in total), if this looks ok? The same color as the one at 3,0 I think.

Ok! Np.

  1. Ok. Are you sure about this? But there is a flag in the warning column at least?

Yes and yes there is a warning.

And to be super clear.. This is what you want:

If a sample has ff<5% then I warn for ncv13,ncv18,ncv21 > 2.5 If a sample has ff>5% then I warn for ncv13,ncv18,ncv21 > 3

Correct?

Thank you for looking at this with such short notice!

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 16 oktober 2018 12:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com<mailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com>mailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se>mailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com>mailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

As always I need some clarification ;) Two question marks:

  1. "In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21."

Do I understand you right if you want me lower the treshold to 2.5, for the samples that have a low fetal fraction only? In that case I wonder how you want that to be visualized. In eg a ncv_13 plot you want the yellow line to vary over the different samples?

  1. "These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow)."

Samples are not automatically flagged yellow. They are set to yellow when you manually classify the sample as suspected.

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alieden commented 6 years ago

ok

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 23 oktober 2018 07:51 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com Kopia: Agne Lieden Agne.Lieden@ki.se; Author author@noreply.github.com Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hi.

Ill push the new version into production and set the new suggestion as a separate issue. I don’t have time to work more on this today unfortunately.

Best,

Maya

23 okt. 2018 kl. 07:40 skrev alieden notifications@github.com<mailto:notifications@github.com>:

This looks correct.

However, perhaps the warning for low ff could be adjusted further as detailed below. This to clarify the warning in relation to the 2% threshold in singleton and 4% in twin pregnancies.

Below 2% = Low FF (all) 2% = Low FF (twin) 3% = Low FF (twin)

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 22 oktober 2018 18:43 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hi!

Okej I changed the threshold for low ff from 2% to 3%.

The new updated version of the code is up and running on https://nipt-stage.scilifelab.se/NIPT/

Its running against our nipt-stage database so you can test things there without effecting production stuff.

Here https://nipt-stage.scilifelab.se/NIPT/batches/BH2375BCX2/ is the batch where I manipulated the data to visualise how the new thresholds work.

Please check that everything is as you wish now. Then Ill put this into production late this afternoon.

Okej?

Best,

Maya

19 okt. 2018 kl. 16:50 skrev alieden notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>>:

This looks correct.

However, I just realized that the best would be if the warning of low ff occurs at 3% or lower. This is becauses 4% is the lowest value allowed for a twin pregnancy i.e good if that is flagged since we only have manual checks for this.

Kr,

Agne

19 okt. 2018 kl. 14:40 skrev mayabrandi notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com>>>:

Okej.

I attach a screen shot where Ive manipulated the ncv18 data and ff data for four samples in our stage database. See if the warnings are as you expect.

19 okt. 2018 kl. 13:23 skrev alieden notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com>>>:

Nej, 2% är den minsta mängd som krävs för godkänd analys med normalfynd.

Jag tycker inte vi behöver flagga låg ff vid 5% (eller lägre) om det inte sammanfaller med ett NCV precis under 3 (som den nya regeln tar hand om).

Inser att det är lite rörigt, bra att du säger till om det inte verkar gå ihop. Vi kan ju faktiskt tänkt galet:)

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 19 oktober 2018 13:13 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com<mailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com<mailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com>>> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se>>>; Author author@noreply.github.com<mailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com%3cmailto:author@noreply.github.com%3cmailto:author@noreply.github.com>>> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hej. Måste bara kolla en grej till. Tröskeln för att varan för "low FF" är i nuläget 2%. Ska jag höja den till 5%?

19 okt. 2018 kl. 07:30 skrev alieden notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com%3cmailto:notifications@github.com>>>:

Yes but the rules should be

If a sample has ff ≤ 5%, then I warn for ncv21 ≥ 2.5

If a sample has ff >5%, then I warn for ncv21 ≥ 3.0

And then the same rules also applied for 13 and 18.

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 18 oktober 2018 13:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com<mailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com<mailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com>>> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se>>>; Author author@noreply.github.com<mailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com%3cmailto:author@noreply.github.com%3cmailto:author@noreply.github.com>>> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

Hi!

  1. There would have to be another warning threshold line at 2,5 (i.e. three upper in total), if this looks ok? The same color as the one at 3,0 I think.

Ok! Np.

  1. Ok. Are you sure about this? But there is a flag in the warning column at least?

Yes and yes there is a warning.

And to be super clear.. This is what you want:

If a sample has ff<5% then I warn for ncv13,ncv18,ncv21 > 2.5 If a sample has ff>5% then I warn for ncv13,ncv18,ncv21 > 3

Correct?

Thank you for looking at this with such short notice!

Från: mayabrandi [mailto:notifications@github.com] Skickat: den 16 oktober 2018 12:44 Till: Clinical-Genomics/NIPT NIPT@noreply.github.com<mailto:NIPT@noreply.github.com<mailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com<mailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com%3cmailto:NIPT@noreply.github.com>>mailto:NIPT@noreply.github.com> Kopia: Agne Lieden Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se<mailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se%3cmailto:Agne.Lieden@ki.se>>mailto:Agne.Lieden@ki.se>; Author author@noreply.github.com<mailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com<mailto:author@noreply.github.com%3cmailto:author@noreply.github.com%3cmailto:author@noreply.github.com%3cmailto:author@noreply.github.com>>mailto:author@noreply.github.com> Ämne: Re: [Clinical-Genomics/NIPT] Enhancement-changed NCV threshold in low (#110)

As always I need some clarification ;) Two question marks:

  1. "In the case of low fetal fraction, 5% or lower, we have decided to (as a precaution) have a lower NCV threshold (2.5 instead of 3.0) for calling a suspected T13/T18/T21."

Do I understand you right if you want me lower the treshold to 2.5, for the samples that have a low fetal fraction only? In that case I wonder how you want that to be visualized. In eg a ncv_13 plot you want the yellow line to vary over the different samples?

  1. "These samples should be flagged the same way as the ones having a NCV in the span from 3.0 to 4.0 (yellow)."

Samples are not automatically flagged yellow. They are set to yellow when you manually classify the sample as suspected.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430190340, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVr8fJ8cYk29ItIPM71VkGMLu4G0Guv0ks5ulbh2gaJpZM4XTgfp. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Clinical-Genomics/NIPT/issues/110#issuecomment-430527286, or mute the thread https://github.com/notifications/unsubscribe-auth/ABPu3e5ig516xdi7yIdEsSjxgmtxBgxHks5uluHugaJpZM4XTgfp.

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mayabrandi commented 6 years ago

@alieden The new version is now in production